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Full Discussion: Sequence extraction
Top Forums Shell Programming and Scripting Sequence extraction Post 302951319 by RudiC on Wednesday 5th of August 2015 06:11:25 AM
Old 08-05-2015
The comments by Don Cragun still apply: most of the sequences are shorter than the coordinates that you have in your file2, and there are coordinates that result in negative string lengths.
On top, none of the samples in file2 match any of those in file1.

How about posting some meaningful samples?
 

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XZDIFF(1)							     XZ Utils								 XZDIFF(1)

NAME
xzcmp, xzdiff, lzcmp, lzdiff - compare compressed files SYNOPSIS
xzcmp [cmp_options] file1 [file2] xzdiff [diff_options] file1 [file2] lzcmp [cmp_options] file1 [file2] lzdiff [diff_options] file1 [file2] DESCRIPTION
xzcmp and xdiff invoke cmp(1) or diff(1) on files compressed with xz(1), lzma(1), gzip(1), or bzip2(1). All options specified are passed directly to cmp or diff. If only one file is specified, then the files compared are file1 (which must have a suffix of a supported com- pression format) and file1 from which the compression format suffix has been stripped. If two files are specified, then they are uncom- pressed if necessary and fed to cmp(1) or diff(1). The exit status from cmp or diff is preserved. The names lzcmp and lzdiff are provided for backward compatibility with LZMA Utils. SEE ALSO
cmp(1), diff(1), xz(1), gzip(1), bzip2(1), zdiff(1) BUGS
Messages from the cmp(1) or diff(1) programs refer to temporary filenames instead of those specified. Tukaani 2009-07-05 XZDIFF(1)
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